I have produced a stacked percent barplot from the following data, which is in a csv file,
,ONE,TWO,THREE
1,2432,420,18
2,276,405,56
3,119,189,110
4,90,163,1
Add + scale_fill_hue(breaks=c("new order 1","new order 2","new order...")) as in:
library(ggplot2)
ggplot(data=PlantGrowth, aes(x=group, fill=group)) + geom_bar() +
geom_bar(colour="black", legend=FALSE) +
scale_fill_hue(breaks=c("trt1","ctrl","trt2"))
I'd also check out http://wiki.stdout.org/rcookbook/Graphs/Legends%20(ggplot2)/ for more.
This may have changed and become easier with he new ggplot but I'm not sure.